Starting phenix.real_space_refine on Tue May 7 17:30:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/05_2024/8qsl_18635_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/05_2024/8qsl_18635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/05_2024/8qsl_18635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/05_2024/8qsl_18635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/05_2024/8qsl_18635_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/05_2024/8qsl_18635_neut.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 48 5.16 5 C 5702 2.51 5 N 1310 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ASP 558": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.21, per 1000 atoms: 0.61 Number of scatterers: 8506 At special positions: 0 Unit cell: (122.265, 80.465, 87.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 2 15.00 O 1444 8.00 N 1310 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG A 604 " - " ASN A 140 " " NAG C 604 " - " ASN C 140 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 81.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 removed outlier: 3.834A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.797A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.981A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.887A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 183 removed outlier: 4.402A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.874A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 3.796A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.610A pdb=" N ALA A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 4.166A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.972A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.059A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.671A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 4.014A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 367 through 395 removed outlier: 4.880A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 4.648A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix removed outlier: 3.917A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.789A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 480 removed outlier: 4.596A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 560 removed outlier: 4.049A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 removed outlier: 4.071A pdb=" N ALA C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 57 removed outlier: 3.771A pdb=" N CYS C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 70 through 98 removed outlier: 3.987A pdb=" N SER C 89 " --> pdb=" O THR C 85 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing helix chain 'C' and resid 101 through 125 removed outlier: 4.200A pdb=" N ALA C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Proline residue: C 121 - end of helix Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 153 through 183 removed outlier: 4.360A pdb=" N THR C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix removed outlier: 3.873A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 220 removed outlier: 3.797A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 248 removed outlier: 3.630A pdb=" N ALA C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) Proline residue: C 229 - end of helix removed outlier: 4.164A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 273 removed outlier: 3.893A pdb=" N MET C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 4.060A pdb=" N GLY C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 347 removed outlier: 3.705A pdb=" N VAL C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) Proline residue: C 323 - end of helix Proline residue: C 330 - end of helix removed outlier: 4.012A pdb=" N VAL C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 367 through 395 removed outlier: 4.824A pdb=" N ASP C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Proline residue: C 382 - end of helix removed outlier: 4.653A pdb=" N ASP C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 390 - end of helix removed outlier: 3.918A pdb=" N HIS C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 431 removed outlier: 3.821A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 Processing helix chain 'C' and resid 454 through 480 removed outlier: 4.608A pdb=" N ILE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 511 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 560 removed outlier: 4.084A pdb=" N TYR C 535 " --> pdb=" O TYR C 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA2, first strand: chain 'C' and resid 435 through 436 594 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1316 1.32 - 1.44: 2295 1.44 - 1.57: 5057 1.57 - 1.69: 4 1.69 - 1.81: 70 Bond restraints: 8742 Sorted by residual: bond pdb=" N GLY A 16 " pdb=" CA GLY A 16 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.36e+00 bond pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" CB GLN C 182 " pdb=" CG GLN C 182 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CB GLN A 182 " pdb=" CG GLN A 182 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.74e-01 bond pdb=" CB LYS A 513 " pdb=" CG LYS A 513 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 ... (remaining 8737 not shown) Histogram of bond angle deviations from ideal: 93.41 - 101.52: 30 101.52 - 109.63: 890 109.63 - 117.74: 5902 117.74 - 125.85: 4962 125.85 - 133.97: 148 Bond angle restraints: 11932 Sorted by residual: angle pdb=" N SER A 255 " pdb=" CA SER A 255 " pdb=" C SER A 255 " ideal model delta sigma weight residual 113.43 108.80 4.63 1.26e+00 6.30e-01 1.35e+01 angle pdb=" N SER C 255 " pdb=" CA SER C 255 " pdb=" C SER C 255 " ideal model delta sigma weight residual 113.43 109.15 4.28 1.26e+00 6.30e-01 1.15e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 113.70 110.57 3.13 9.50e-01 1.11e+00 1.08e+01 angle pdb=" OG1 THR C 359 " pdb=" CB THR C 359 " pdb=" CG2 THR C 359 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.93e+00 angle pdb=" OG1 THR C 358 " pdb=" CB THR C 358 " pdb=" CG2 THR C 358 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.90e+00 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 5472 30.78 - 61.56: 246 61.56 - 92.34: 14 92.34 - 123.12: 0 123.12 - 153.90: 2 Dihedral angle restraints: 5734 sinusoidal: 2742 harmonic: 2992 Sorted by residual: dihedral pdb=" CA GLY C 396 " pdb=" C GLY C 396 " pdb=" N LEU C 397 " pdb=" CA LEU C 397 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" N LEU A 397 " pdb=" CA LEU A 397 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C3 PGT A 608 " pdb=" C1 PGT A 608 " pdb=" C2 PGT A 608 " pdb=" O3P PGT A 608 " ideal model delta sinusoidal sigma weight residual -66.13 87.77 -153.90 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1029 0.034 - 0.067: 260 0.067 - 0.101: 88 0.101 - 0.135: 15 0.135 - 0.169: 6 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB THR C 358 " pdb=" CA THR C 358 " pdb=" OG1 THR C 358 " pdb=" CG2 THR C 358 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CB THR C 359 " pdb=" CA THR C 359 " pdb=" OG1 THR C 359 " pdb=" CG2 THR C 359 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB THR A 359 " pdb=" CA THR A 359 " pdb=" OG1 THR A 359 " pdb=" CG2 THR A 359 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 1395 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 452 " 0.019 2.00e-02 2.50e+03 1.49e-02 5.57e+00 pdb=" CG TRP C 452 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 452 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 452 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 452 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 452 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 452 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 452 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 452 " 0.017 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP A 452 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 452 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 452 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 452 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 452 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 452 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 452 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 452 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 356 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ASN A 356 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN A 356 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 357 " 0.010 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 96 2.55 - 3.14: 7830 3.14 - 3.73: 13398 3.73 - 4.31: 17834 4.31 - 4.90: 29454 Nonbonded interactions: 68612 Sorted by model distance: nonbonded pdb=" O ALA A 227 " pdb=" OG1 THR A 230 " model vdw 1.968 2.440 nonbonded pdb=" O ALA C 227 " pdb=" OG1 THR C 230 " model vdw 1.973 2.440 nonbonded pdb=" O GLN C 218 " pdb=" NE2 GLN C 218 " model vdw 2.037 2.520 nonbonded pdb=" OG SER A 346 " pdb=" OE1 GLN A 454 " model vdw 2.063 2.440 nonbonded pdb=" OG SER C 346 " pdb=" OE1 GLN C 454 " model vdw 2.067 2.440 ... (remaining 68607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.910 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8742 Z= 0.236 Angle : 0.671 8.420 11932 Z= 0.350 Chirality : 0.036 0.169 1398 Planarity : 0.004 0.032 1410 Dihedral : 15.580 153.903 3806 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.12 % Allowed : 25.85 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 1038 helix: 2.28 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -2.92 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 452 HIS 0.004 0.001 HIS C 348 PHE 0.017 0.001 PHE A 194 TYR 0.006 0.001 TYR C 86 ARG 0.002 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ASP cc_start: 0.7764 (t0) cc_final: 0.7512 (t0) REVERT: C 373 ASP cc_start: 0.7789 (t0) cc_final: 0.7505 (t0) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.7384 time to fit residues: 154.7481 Evaluate side-chains 156 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8742 Z= 0.239 Angle : 0.749 7.957 11932 Z= 0.359 Chirality : 0.040 0.206 1398 Planarity : 0.005 0.040 1410 Dihedral : 11.453 149.688 2106 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.41 % Allowed : 24.39 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1038 helix: 2.21 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -2.56 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 452 HIS 0.002 0.001 HIS C 521 PHE 0.023 0.002 PHE A 194 TYR 0.011 0.001 TYR C 226 ARG 0.004 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8444 (mm) REVERT: C 226 TYR cc_start: 0.8208 (m-80) cc_final: 0.7523 (m-80) outliers start: 28 outliers final: 7 residues processed: 188 average time/residue: 0.7446 time to fit residues: 154.9859 Evaluate side-chains 166 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 401 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 218 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8742 Z= 0.215 Angle : 0.770 10.158 11932 Z= 0.355 Chirality : 0.042 0.400 1398 Planarity : 0.004 0.054 1410 Dihedral : 11.368 146.714 2106 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.88 % Allowed : 24.27 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1038 helix: 2.15 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -2.61 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 453 HIS 0.003 0.001 HIS C 559 PHE 0.018 0.001 PHE A 325 TYR 0.023 0.001 TYR A 226 ARG 0.003 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7841 (tp) REVERT: C 215 TYR cc_start: 0.7671 (t80) cc_final: 0.7459 (t80) REVERT: C 226 TYR cc_start: 0.8309 (m-80) cc_final: 0.7628 (m-80) REVERT: C 371 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6239 (ptm) outliers start: 40 outliers final: 15 residues processed: 209 average time/residue: 0.6248 time to fit residues: 146.5765 Evaluate side-chains 175 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 356 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 8742 Z= 0.214 Angle : 0.754 10.415 11932 Z= 0.347 Chirality : 0.043 0.383 1398 Planarity : 0.004 0.049 1410 Dihedral : 11.185 144.798 2106 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.34 % Allowed : 24.27 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.28), residues: 1038 helix: 2.06 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.61 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 452 HIS 0.002 0.001 HIS C 559 PHE 0.027 0.001 PHE A 550 TYR 0.026 0.001 TYR A 226 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 182 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8184 (t) REVERT: C 154 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8183 (t) REVERT: C 215 TYR cc_start: 0.7612 (t80) cc_final: 0.7402 (t80) REVERT: C 222 PHE cc_start: 0.8103 (m-80) cc_final: 0.7721 (m-80) REVERT: C 226 TYR cc_start: 0.8337 (m-80) cc_final: 0.7476 (m-80) REVERT: C 371 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6260 (ptm) outliers start: 52 outliers final: 24 residues processed: 212 average time/residue: 0.6346 time to fit residues: 150.6819 Evaluate side-chains 183 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 0.0370 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8742 Z= 0.219 Angle : 0.808 11.767 11932 Z= 0.366 Chirality : 0.050 0.537 1398 Planarity : 0.004 0.047 1410 Dihedral : 11.159 143.610 2106 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.74 % Favored : 93.06 % Rotamer: Outliers : 5.73 % Allowed : 26.95 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.28), residues: 1038 helix: 2.04 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.70 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 452 HIS 0.001 0.001 HIS A 560 PHE 0.038 0.001 PHE C 550 TYR 0.006 0.001 TYR A 226 ARG 0.001 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 297 ASP cc_start: 0.6076 (OUTLIER) cc_final: 0.5762 (p0) REVERT: C 154 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8154 (t) REVERT: C 215 TYR cc_start: 0.7601 (t80) cc_final: 0.7391 (t80) REVERT: C 218 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8280 (mm-40) REVERT: C 244 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7586 (tp40) REVERT: C 371 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6174 (ptm) outliers start: 47 outliers final: 19 residues processed: 198 average time/residue: 0.7098 time to fit residues: 155.7339 Evaluate side-chains 172 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8742 Z= 0.232 Angle : 0.808 12.404 11932 Z= 0.361 Chirality : 0.046 0.376 1398 Planarity : 0.004 0.042 1410 Dihedral : 11.065 142.276 2106 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.74 % Favored : 93.06 % Rotamer: Outliers : 4.88 % Allowed : 28.05 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.28), residues: 1038 helix: 2.01 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.66 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 452 HIS 0.001 0.000 HIS C 395 PHE 0.026 0.001 PHE C 550 TYR 0.009 0.001 TYR C 226 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5678 (p0) REVERT: A 371 MET cc_start: 0.6883 (ttm) cc_final: 0.6581 (ttm) REVERT: C 154 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8200 (t) REVERT: C 215 TYR cc_start: 0.7574 (t80) cc_final: 0.7355 (t80) REVERT: C 218 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8357 (mm-40) REVERT: C 371 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6172 (ptm) outliers start: 40 outliers final: 22 residues processed: 197 average time/residue: 0.7142 time to fit residues: 156.6970 Evaluate side-chains 177 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 457 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.0470 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8742 Z= 0.220 Angle : 0.824 13.141 11932 Z= 0.368 Chirality : 0.045 0.370 1398 Planarity : 0.004 0.045 1410 Dihedral : 10.913 140.842 2106 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 4.63 % Allowed : 28.78 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 1038 helix: 1.92 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.64 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 452 HIS 0.001 0.000 HIS C 521 PHE 0.018 0.001 PHE C 536 TYR 0.021 0.001 TYR C 226 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5609 (p0) REVERT: A 371 MET cc_start: 0.6828 (ttm) cc_final: 0.6502 (ttm) REVERT: C 154 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8214 (t) REVERT: C 215 TYR cc_start: 0.7490 (t80) cc_final: 0.7274 (t80) REVERT: C 218 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8313 (mm-40) outliers start: 38 outliers final: 23 residues processed: 192 average time/residue: 0.6904 time to fit residues: 147.4508 Evaluate side-chains 177 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 457 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.0770 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8742 Z= 0.229 Angle : 0.826 12.816 11932 Z= 0.370 Chirality : 0.045 0.374 1398 Planarity : 0.004 0.045 1410 Dihedral : 10.827 139.717 2106 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.27 % Allowed : 30.49 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 1038 helix: 1.91 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.69 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 453 HIS 0.002 0.000 HIS A 348 PHE 0.017 0.001 PHE C 536 TYR 0.045 0.001 TYR C 226 ARG 0.001 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6082 (OUTLIER) cc_final: 0.5612 (p0) REVERT: C 154 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8233 (t) outliers start: 35 outliers final: 24 residues processed: 189 average time/residue: 0.6980 time to fit residues: 146.3835 Evaluate side-chains 172 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8742 Z= 0.235 Angle : 0.850 13.472 11932 Z= 0.382 Chirality : 0.045 0.409 1398 Planarity : 0.004 0.053 1410 Dihedral : 10.670 138.485 2106 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.90 % Allowed : 31.46 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 1038 helix: 1.87 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.73 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 452 HIS 0.002 0.001 HIS A 348 PHE 0.017 0.001 PHE C 536 TYR 0.035 0.001 TYR C 226 ARG 0.005 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: 0.8324 (m-10) cc_final: 0.7941 (m-10) REVERT: A 297 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5560 (p0) REVERT: A 307 PHE cc_start: 0.5960 (m-80) cc_final: 0.5681 (m-80) REVERT: C 154 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8246 (t) REVERT: C 215 TYR cc_start: 0.7517 (t80) cc_final: 0.7298 (t80) outliers start: 32 outliers final: 22 residues processed: 175 average time/residue: 0.7272 time to fit residues: 141.0539 Evaluate side-chains 170 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8742 Z= 0.278 Angle : 0.874 12.949 11932 Z= 0.393 Chirality : 0.046 0.383 1398 Planarity : 0.004 0.048 1410 Dihedral : 10.554 137.281 2106 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.05 % Allowed : 33.29 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 1038 helix: 1.83 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.82 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 452 HIS 0.002 0.001 HIS C 348 PHE 0.014 0.002 PHE A 194 TYR 0.031 0.001 TYR C 226 ARG 0.005 0.000 ARG A 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5498 (p0) REVERT: A 307 PHE cc_start: 0.5948 (m-80) cc_final: 0.5657 (m-80) REVERT: C 154 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8334 (t) REVERT: C 218 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8244 (mm-40) outliers start: 25 outliers final: 20 residues processed: 174 average time/residue: 0.7547 time to fit residues: 145.3492 Evaluate side-chains 164 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 401 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.136806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109113 restraints weight = 16915.581| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.34 r_work: 0.3602 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8742 Z= 0.260 Angle : 0.884 12.918 11932 Z= 0.401 Chirality : 0.047 0.392 1398 Planarity : 0.004 0.050 1410 Dihedral : 10.422 136.142 2106 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.17 % Allowed : 33.66 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1038 helix: 1.79 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.88 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 368 HIS 0.003 0.001 HIS C 303 PHE 0.021 0.001 PHE C 550 TYR 0.019 0.001 TYR C 226 ARG 0.005 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2993.53 seconds wall clock time: 54 minutes 32.87 seconds (3272.87 seconds total)